Scott,
I finally got around to check follow your instructions, but I ran into this problem:
----------------------------------------------------------------- Parsed document of type Plugin -----------------------------------------------------------------
Plugin: CarpetHDF5 ("Carpet AMR/curvilinear HDF5 output generated by the Cactus Computational Toolkit", type=database) -- version 2.1 Attribute: ()
-- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Checking whether CXX compiler has -isysroot -- Checking whether CXX compiler has -isysroot - yes -- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done CMake Error at CMakeLists.txt:90 (VISIT_PLUGIN_TARGET_RTOD): Unknown CMake command "VISIT_PLUGIN_TARGET_RTOD".
-- Configuring incomplete, errors occurred! make: *** No targets specified and no makefile found. Stop.
The only difference was that I did a ./configure --enable-cxx first in my hdf5-1.8.9 directory.
Could you please help me out?
Christian, do you have any suggestions?
thanks, Maria ________________________________________ From: Babiuc-Hamilton, Maria Sent: Tuesday, May 15, 2012 8:42 AM To: Scott Hawley Subject: Re: [Users] How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS X Lion
Scott,
Fantastic! I'll try it right away! I had problems making Visit work with MacOS last year, and had to do my own little hack, but haven't use it for a while, because I was afraid that if I upgrade I'll run into problems again. Have had any success with ygraph?
Cheers, Maria
On 5/14/12 5:23 PM, "Scott Hawley" scott.hawley@belmont.edu wrote:
Here's what I did:
- Downloaded the 64-bit binary of Visit 2.4.2 from the Visit web site
- Downloaded the CarpetHDF directory via svn.
- Downloaded hdf5-1.8.9 source via ftp. I just put it in the CarpetHDF5
directory. Did a make and make installŠ. "HDF5 Directory" is then .../hdf5-1.8.9/hdf5/ (see below) 4. Made sure "Remote Login" is enabled under "Sharing" in "System Preferences". Visit uses this. Went ahead and did a "ssh localhost" just to make sure. I was actually prompted to confirm an address because I'm on LSU's network right now. (Presumably Visit needs a clean login with no pesky questions or password prompts.) 5. Created symbolic links in /usr/lib to whichever MPI libraries I planned to use. Older versions of OS X had native MPI support, and this is hard coded in the binary you get from the visit site. I use OpenMPI and MacPorts, so I went to /usr/lib and did "sudo ln -s /opt/local/lib/libmpi* ." 6. Deleted my ~/.visit directory entirely. This may not be necessary. 7. Went in the CarpetHDF5 and ran ./install and Šbasically just did what was in the readme, that is: in the xmledit window, clicked on "Cmake" and then updated the flags, as in
CXXFLAGS = -I/Applications/VisIt.app/Contents/Resources/2.4.2/darwin-x86_64/include -I/Users/shawley/apps/VizTools/CarpetHDF5/hdf5-1.8.9/hdf5/include LDFLAGS = -L/Applications/VisIt.app/Contents/Resources/2.4.2/darwin-x86_64/lib -L/Users/shawley/apps/VizTools/CarpetHDF5/hdf5-1.8.9/hdf5/lib Saved and closed the window, let it do its thing... 8. Ran visit from the command line, using the -noconfig option. The latest version of Visit has a problem with "localhost" on Mac, for some reason. so visit -noconfig
..and then visit came up, I opened a .h5 file and was able to do all the usual things with it!
Good luck! -Scott
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Yes, I remember seeing that error too; although it may have only been with version 2.5 that I saw that.
So apparently some other libraries also used to be native, and are no longer, and I had already created the other links.
So in addition to lipmpi*, you'll also want to do
% cd /usr/lib/; sudo ln -s /opt/local/lib/libopen-pal* /opt/local/lib/libopen-rte* .
Let me know if that helps.
On 5/21/12 2:11 PM, "Babiuc-Hamilton, Maria" babiuc@marshall.edu wrote:
Scott,
I finally got around to check follow your instructions, but I ran into this problem:
Parsed document of type Plugin
Plugin: CarpetHDF5 ("Carpet AMR/curvilinear HDF5 output generated by the Cactus Computational Toolkit", type=database) -- version 2.1 Attribute: ()
-- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Checking whether CXX compiler has -isysroot -- Checking whether CXX compiler has -isysroot - yes -- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done CMake Error at CMakeLists.txt:90 (VISIT_PLUGIN_TARGET_RTOD): Unknown CMake command "VISIT_PLUGIN_TARGET_RTOD".
-- Configuring incomplete, errors occurred! make: *** No targets specified and no makefile found. Stop.
The only difference was that I did a ./configure --enable-cxx first in my hdf5-1.8.9 directory.
Could you please help me out?
Christian, do you have any suggestions?
thanks, Maria ________________________________________ From: Babiuc-Hamilton, Maria Sent: Tuesday, May 15, 2012 8:42 AM To: Scott Hawley Subject: Re: [Users] How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS X Lion
Scott,
Fantastic! I'll try it right away! I had problems making Visit work with MacOS last year, and had to do my own little hack, but haven't use it for a while, because I was afraid that if I upgrade I'll run into problems again. Have had any success with ygraph?
Cheers, Maria
On 5/14/12 5:23 PM, "Scott Hawley" scott.hawley@belmont.edu wrote:
Here's what I did:
- Downloaded the 64-bit binary of Visit 2.4.2 from the Visit web site
- Downloaded the CarpetHDF directory via svn.
- Downloaded hdf5-1.8.9 source via ftp. I just put it in the CarpetHDF5
directory. Did a make and make installŠ. "HDF5 Directory" is then .../hdf5-1.8.9/hdf5/ (see below) 4. Made sure "Remote Login" is enabled under "Sharing" in "System Preferences". Visit uses this. Went ahead and did a "ssh localhost" just to make sure. I was actually prompted to confirm an address because I'm on LSU's network right now. (Presumably Visit needs a clean login with no pesky questions or password prompts.) 5. Created symbolic links in /usr/lib to whichever MPI libraries I planned to use. Older versions of OS X had native MPI support, and this is hard coded in the binary you get from the visit site. I use OpenMPI and MacPorts, so I went to /usr/lib and did "sudo ln -s /opt/local/lib/libmpi* ." 6. Deleted my ~/.visit directory entirely. This may not be necessary. 7. Went in the CarpetHDF5 and ran ./install and Šbasically just did what was in the readme, that is: in the xmledit window, clicked on "Cmake" and then updated the flags, as in
CXXFLAGS = -I/Applications/VisIt.app/Contents/Resources/2.4.2/darwin-x86_64/include -I/Users/shawley/apps/VizTools/CarpetHDF5/hdf5-1.8.9/hdf5/include LDFLAGS = -L/Applications/VisIt.app/Contents/Resources/2.4.2/darwin-x86_64/lib -L/Users/shawley/apps/VizTools/CarpetHDF5/hdf5-1.8.9/hdf5/lib Saved and closed the window, let it do its thing... 8. Ran visit from the command line, using the -noconfig option. The latest version of Visit has a problem with "localhost" on Mac, for some reason. so visit -noconfig
..and then visit came up, I opened a .h5 file and was able to do all the usual things with it!
Good luck! -Scott
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Thanks. I just downgraded to Visit 2.4.2 and now it looked like I got rid of that error. However, when trying to see a h5 file, I got the error:
The metadata server running on host localhost has exited abnormally. VisIt is trying to restart it.
Shortly thereafter, the following occured...
VisIt was unable to open "/Users/student/Cactus/VizTools/ks-mclachlan_metric.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the underlying file format has changed and VisIt's readers have not been updated yet, or when the reader VisIt is using for your file format is not robust. Please check whether the file is corrupted and, if not, contact a VisIt developer.
Moreover, when I am trying to run Cactus, I am getting this:
./cactus_tov tov.rpar dyld: Symbol not found: __ZN3MPI3Win14Set_errhandlerERKNS_10ErrhandlerE Referenced from: /Users/student/Cactus/exe/./cactus_tov Expected in: /usr/lib/libmpi_cxx.0.dylib
Trace/BPT trap
I checked, and I do have /usr/lib/libmpi_cxx.0.dylib Any ideas?
thanks, Maria
________________________________________ From: Scott Hawley [scott.hawley@belmont.edu] Sent: Monday, May 21, 2012 3:18 PM To: Babiuc-Hamilton, Maria Cc: users@einsteintoolkit.org Subject: Re: Follow-up: [Users] How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS X Lion
Yes, I remember seeing that error too; although it may have only been with version 2.5 that I saw that.
So apparently some other libraries also used to be native, and are no longer, and I had already created the other links.
So in addition to lipmpi*, you'll also want to do
% cd /usr/lib/; sudo ln -s /opt/local/lib/libopen-pal* /opt/local/lib/libopen-rte* .
Let me know if that helps.
On 5/21/12 2:11 PM, "Babiuc-Hamilton, Maria" babiuc@marshall.edu wrote:
Scott,
I finally got around to check follow your instructions, but I ran into this problem:
Parsed document of type Plugin
Plugin: CarpetHDF5 ("Carpet AMR/curvilinear HDF5 output generated by the Cactus Computational Toolkit", type=database) -- version 2.1 Attribute: ()
-- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Checking whether CXX compiler has -isysroot -- Checking whether CXX compiler has -isysroot - yes -- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done CMake Error at CMakeLists.txt:90 (VISIT_PLUGIN_TARGET_RTOD): Unknown CMake command "VISIT_PLUGIN_TARGET_RTOD".
-- Configuring incomplete, errors occurred! make: *** No targets specified and no makefile found. Stop.
The only difference was that I did a ./configure --enable-cxx first in my hdf5-1.8.9 directory.
Could you please help me out?
Christian, do you have any suggestions?
thanks, Maria ________________________________________ From: Babiuc-Hamilton, Maria Sent: Tuesday, May 15, 2012 8:42 AM To: Scott Hawley Subject: Re: [Users] How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS X Lion
Scott,
Fantastic! I'll try it right away! I had problems making Visit work with MacOS last year, and had to do my own little hack, but haven't use it for a while, because I was afraid that if I upgrade I'll run into problems again. Have had any success with ygraph?
Cheers, Maria
On 5/14/12 5:23 PM, "Scott Hawley" scott.hawley@belmont.edu wrote:
Here's what I did:
- Downloaded the 64-bit binary of Visit 2.4.2 from the Visit web site
- Downloaded the CarpetHDF directory via svn.
- Downloaded hdf5-1.8.9 source via ftp. I just put it in the CarpetHDF5
directory. Did a make and make installŠ. "HDF5 Directory" is then .../hdf5-1.8.9/hdf5/ (see below) 4. Made sure "Remote Login" is enabled under "Sharing" in "System Preferences". Visit uses this. Went ahead and did a "ssh localhost" just to make sure. I was actually prompted to confirm an address because I'm on LSU's network right now. (Presumably Visit needs a clean login with no pesky questions or password prompts.) 5. Created symbolic links in /usr/lib to whichever MPI libraries I planned to use. Older versions of OS X had native MPI support, and this is hard coded in the binary you get from the visit site. I use OpenMPI and MacPorts, so I went to /usr/lib and did "sudo ln -s /opt/local/lib/libmpi* ." 6. Deleted my ~/.visit directory entirely. This may not be necessary. 7. Went in the CarpetHDF5 and ran ./install and Šbasically just did what was in the readme, that is: in the xmledit window, clicked on "Cmake" and then updated the flags, as in
CXXFLAGS = -I/Applications/VisIt.app/Contents/Resources/2.4.2/darwin-x86_64/include -I/Users/shawley/apps/VizTools/CarpetHDF5/hdf5-1.8.9/hdf5/include LDFLAGS = -L/Applications/VisIt.app/Contents/Resources/2.4.2/darwin-x86_64/lib -L/Users/shawley/apps/VizTools/CarpetHDF5/hdf5-1.8.9/hdf5/lib Saved and closed the window, let it do its thing... 8. Ran visit from the command line, using the -noconfig option. The latest version of Visit has a problem with "localhost" on Mac, for some reason. so visit -noconfig
..and then visit came up, I opened a .h5 file and was able to do all the usual things with it!
Good luck! -Scott
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
You compiled the CarpetHDF plugin like I said, and are running visit with -noconfig?
On 5/21/12 3:03 PM, "Babiuc-Hamilton, Maria" babiuc@marshall.edu wrote:
Thanks. I just downgraded to Visit 2.4.2 and now it looked like I got rid of that error. However, when trying to see a h5 file, I got the error:
The metadata server running on host localhost has exited abnormally. VisIt is trying to restart it.
Shortly thereafter, the following occured...
VisIt was unable to open "/Users/student/Cactus/VizTools/ks-mclachlan_metric.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the underlying file format has changed and VisIt's readers have not been updated yet, or when the reader VisIt is using for your file format is not robust. Please check whether the file is corrupted and, if not, contact a VisIt developer.
Moreover, when I am trying to run Cactus, I am getting this:
./cactus_tov tov.rpar dyld: Symbol not found: __ZN3MPI3Win14Set_errhandlerERKNS_10ErrhandlerE Referenced from: /Users/student/Cactus/exe/./cactus_tov Expected in: /usr/lib/libmpi_cxx.0.dylib
Trace/BPT trap
I checked, and I do have /usr/lib/libmpi_cxx.0.dylib Any ideas?
thanks, Maria
From: Scott Hawley [scott.hawley@belmont.edu] Sent: Monday, May 21, 2012 3:18 PM To: Babiuc-Hamilton, Maria Cc: users@einsteintoolkit.org Subject: Re: Follow-up: [Users] How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS X Lion
Yes, I remember seeing that error too; although it may have only been with version 2.5 that I saw that.
So apparently some other libraries also used to be native, and are no longer, and I had already created the other links.
So in addition to lipmpi*, you'll also want to do
% cd /usr/lib/; sudo ln -s /opt/local/lib/libopen-pal* /opt/local/lib/libopen-rte* .
Let me know if that helps.
On 5/21/12 2:11 PM, "Babiuc-Hamilton, Maria" babiuc@marshall.edu wrote:
Scott,
I finally got around to check follow your instructions, but I ran into this problem:
Parsed document of type Plugin
Plugin: CarpetHDF5 ("Carpet AMR/curvilinear HDF5 output generated by the Cactus Computational Toolkit", type=database) -- version 2.1 Attribute: ()
-- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Checking whether CXX compiler has -isysroot -- Checking whether CXX compiler has -isysroot - yes -- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done CMake Error at CMakeLists.txt:90 (VISIT_PLUGIN_TARGET_RTOD): Unknown CMake command "VISIT_PLUGIN_TARGET_RTOD".
-- Configuring incomplete, errors occurred! make: *** No targets specified and no makefile found. Stop.
The only difference was that I did a ./configure --enable-cxx first in my hdf5-1.8.9 directory.
Could you please help me out?
Christian, do you have any suggestions?
thanks, Maria ________________________________________ From: Babiuc-Hamilton, Maria Sent: Tuesday, May 15, 2012 8:42 AM To: Scott Hawley Subject: Re: [Users] How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS X Lion
Scott,
Fantastic! I'll try it right away! I had problems making Visit work with MacOS last year, and had to do my own little hack, but haven't use it for a while, because I was afraid that if I upgrade I'll run into problems again. Have had any success with ygraph?
Cheers, Maria
On 5/14/12 5:23 PM, "Scott Hawley" scott.hawley@belmont.edu wrote:
Here's what I did:
- Downloaded the 64-bit binary of Visit 2.4.2 from the Visit web site
- Downloaded the CarpetHDF directory via svn.
- Downloaded hdf5-1.8.9 source via ftp. I just put it in the
CarpetHDF5 directory. Did a make and make installŠ. "HDF5 Directory" is then .../hdf5-1.8.9/hdf5/ (see below) 4. Made sure "Remote Login" is enabled under "Sharing" in "System Preferences". Visit uses this. Went ahead and did a "ssh localhost" just to make sure. I was actually prompted to confirm an address because I'm on LSU's network right now. (Presumably Visit needs a clean login with no pesky questions or password prompts.) 5. Created symbolic links in /usr/lib to whichever MPI libraries I planned to use. Older versions of OS X had native MPI support, and this is hard coded in the binary you get from the visit site. I use OpenMPI and MacPorts, so I went to /usr/lib and did "sudo ln -s /opt/local/lib/libmpi* ." 6. Deleted my ~/.visit directory entirely. This may not be necessary. 7. Went in the CarpetHDF5 and ran ./install and Šbasically just did what was in the readme, that is: in the xmledit window, clicked on "Cmake" and then updated the flags, as in
CXXFLAGS = -I/Applications/VisIt.app/Contents/Resources/2.4.2/darwin-x86_64/include -I/Users/shawley/apps/VizTools/CarpetHDF5/hdf5-1.8.9/hdf5/include LDFLAGS = -L/Applications/VisIt.app/Contents/Resources/2.4.2/darwin-x86_64/lib -L/Users/shawley/apps/VizTools/CarpetHDF5/hdf5-1.8.9/hdf5/lib Saved and closed the window, let it do its thing... 8. Ran visit from the command line, using the -noconfig option. The latest version of Visit has a problem with "localhost" on Mac, for some reason. so visit -noconfig
..and then visit came up, I opened a .h5 file and was able to do all the usual things with it!
Good luck! -Scott
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Scott,
Yes, I did. The error I am getting now when configuring Cactus is: dyld: Symbol not found: _orte_ess Referenced from: /usr/local/lib/libmpi.0.dylib Expected in: /usr/local/lib/libopen-rte.0.dylib in /usr/local/lib/libmpi.0.dylib
Looking on the web, it seems that other Apple users had this problem when trying to link libraries. I'm afraid that I made this mess when I linked libopen-rte*? Is there a clean and quick fix, or I need to reinstall my whole operating system? :O
Please help! Maria
________________________________________ From: Scott Hawley [scott.hawley@belmont.edu] Sent: Monday, May 21, 2012 4:05 PM To: Babiuc-Hamilton, Maria Cc: users@einsteintoolkit.org Subject: Re: Follow-up: [Users] How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS X Lion
You compiled the CarpetHDF plugin like I said, and are running visit with -noconfig?
On 5/21/12 3:03 PM, "Babiuc-Hamilton, Maria" babiuc@marshall.edu wrote:
Thanks. I just downgraded to Visit 2.4.2 and now it looked like I got rid of that error. However, when trying to see a h5 file, I got the error:
The metadata server running on host localhost has exited abnormally. VisIt is trying to restart it.
Shortly thereafter, the following occured...
VisIt was unable to open "/Users/student/Cactus/VizTools/ks-mclachlan_metric.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the underlying file format has changed and VisIt's readers have not been updated yet, or when the reader VisIt is using for your file format is not robust. Please check whether the file is corrupted and, if not, contact a VisIt developer.
Moreover, when I am trying to run Cactus, I am getting this:
./cactus_tov tov.rpar dyld: Symbol not found: __ZN3MPI3Win14Set_errhandlerERKNS_10ErrhandlerE Referenced from: /Users/student/Cactus/exe/./cactus_tov Expected in: /usr/lib/libmpi_cxx.0.dylib
Trace/BPT trap
I checked, and I do have /usr/lib/libmpi_cxx.0.dylib Any ideas?
thanks, Maria
From: Scott Hawley [scott.hawley@belmont.edu] Sent: Monday, May 21, 2012 3:18 PM To: Babiuc-Hamilton, Maria Cc: users@einsteintoolkit.org Subject: Re: Follow-up: [Users] How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS X Lion
Yes, I remember seeing that error too; although it may have only been with version 2.5 that I saw that.
So apparently some other libraries also used to be native, and are no longer, and I had already created the other links.
So in addition to lipmpi*, you'll also want to do
% cd /usr/lib/; sudo ln -s /opt/local/lib/libopen-pal* /opt/local/lib/libopen-rte* .
Let me know if that helps.
On 5/21/12 2:11 PM, "Babiuc-Hamilton, Maria" babiuc@marshall.edu wrote:
Scott,
I finally got around to check follow your instructions, but I ran into this problem:
Parsed document of type Plugin
Plugin: CarpetHDF5 ("Carpet AMR/curvilinear HDF5 output generated by the Cactus Computational Toolkit", type=database) -- version 2.1 Attribute: ()
-- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Checking whether CXX compiler has -isysroot -- Checking whether CXX compiler has -isysroot - yes -- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done CMake Error at CMakeLists.txt:90 (VISIT_PLUGIN_TARGET_RTOD): Unknown CMake command "VISIT_PLUGIN_TARGET_RTOD".
-- Configuring incomplete, errors occurred! make: *** No targets specified and no makefile found. Stop.
The only difference was that I did a ./configure --enable-cxx first in my hdf5-1.8.9 directory.
Could you please help me out?
Christian, do you have any suggestions?
thanks, Maria ________________________________________ From: Babiuc-Hamilton, Maria Sent: Tuesday, May 15, 2012 8:42 AM To: Scott Hawley Subject: Re: [Users] How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS X Lion
Scott,
Fantastic! I'll try it right away! I had problems making Visit work with MacOS last year, and had to do my own little hack, but haven't use it for a while, because I was afraid that if I upgrade I'll run into problems again. Have had any success with ygraph?
Cheers, Maria
On 5/14/12 5:23 PM, "Scott Hawley" scott.hawley@belmont.edu wrote:
Here's what I did:
- Downloaded the 64-bit binary of Visit 2.4.2 from the Visit web site
- Downloaded the CarpetHDF directory via svn.
- Downloaded hdf5-1.8.9 source via ftp. I just put it in the
CarpetHDF5 directory. Did a make and make installŠ. "HDF5 Directory" is then .../hdf5-1.8.9/hdf5/ (see below) 4. Made sure "Remote Login" is enabled under "Sharing" in "System Preferences". Visit uses this. Went ahead and did a "ssh localhost" just to make sure. I was actually prompted to confirm an address because I'm on LSU's network right now. (Presumably Visit needs a clean login with no pesky questions or password prompts.) 5. Created symbolic links in /usr/lib to whichever MPI libraries I planned to use. Older versions of OS X had native MPI support, and this is hard coded in the binary you get from the visit site. I use OpenMPI and MacPorts, so I went to /usr/lib and did "sudo ln -s /opt/local/lib/libmpi* ." 6. Deleted my ~/.visit directory entirely. This may not be necessary. 7. Went in the CarpetHDF5 and ran ./install and Šbasically just did what was in the readme, that is: in the xmledit window, clicked on "Cmake" and then updated the flags, as in
CXXFLAGS = -I/Applications/VisIt.app/Contents/Resources/2.4.2/darwin-x86_64/include -I/Users/shawley/apps/VizTools/CarpetHDF5/hdf5-1.8.9/hdf5/include LDFLAGS = -L/Applications/VisIt.app/Contents/Resources/2.4.2/darwin-x86_64/lib -L/Users/shawley/apps/VizTools/CarpetHDF5/hdf5-1.8.9/hdf5/lib Saved and closed the window, let it do its thing... 8. Ran visit from the command line, using the -noconfig option. The latest version of Visit has a problem with "localhost" on Mac, for some reason. so visit -noconfig
..and then visit came up, I opened a .h5 file and was able to do all the usual things with it!
Good luck! -Scott
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Maria, No there are only a few libopen-rte files you can unlink if you want.
I noticed that these errors are coming from /usr/local/lib, which is not a location I've used. I put the links in /usr/lib.
On 5/22/12 9:06 AM, "Babiuc-Hamilton, Maria" babiuc@marshall.edu wrote:
Scott,
Yes, I did. The error I am getting now when configuring Cactus is: dyld: Symbol not found: _orte_ess Referenced from: /usr/local/lib/libmpi.0.dylib Expected in: /usr/local/lib/libopen-rte.0.dylib in /usr/local/lib/libmpi.0.dylib
Looking on the web, it seems that other Apple users had this problem when trying to link libraries. I'm afraid that I made this mess when I linked libopen-rte*? Is there a clean and quick fix, or I need to reinstall my whole operating system? :O
Please help! Maria
From: Scott Hawley [scott.hawley@belmont.edu] Sent: Monday, May 21, 2012 4:05 PM To: Babiuc-Hamilton, Maria Cc: users@einsteintoolkit.org Subject: Re: Follow-up: [Users] How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS X Lion
You compiled the CarpetHDF plugin like I said, and are running visit with -noconfig?
On 5/21/12 3:03 PM, "Babiuc-Hamilton, Maria" babiuc@marshall.edu wrote:
Thanks. I just downgraded to Visit 2.4.2 and now it looked like I got rid of that error. However, when trying to see a h5 file, I got the error:
The metadata server running on host localhost has exited abnormally. VisIt is trying to restart it.
Shortly thereafter, the following occured...
VisIt was unable to open "/Users/student/Cactus/VizTools/ks-mclachlan_metric.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the underlying file format has changed and VisIt's readers have not been updated yet, or when the reader VisIt is using for your file format is not robust. Please check whether the file is corrupted and, if not, contact a VisIt developer.
Moreover, when I am trying to run Cactus, I am getting this:
./cactus_tov tov.rpar dyld: Symbol not found: __ZN3MPI3Win14Set_errhandlerERKNS_10ErrhandlerE Referenced from: /Users/student/Cactus/exe/./cactus_tov Expected in: /usr/lib/libmpi_cxx.0.dylib
Trace/BPT trap
I checked, and I do have /usr/lib/libmpi_cxx.0.dylib Any ideas?
thanks, Maria
From: Scott Hawley [scott.hawley@belmont.edu] Sent: Monday, May 21, 2012 3:18 PM To: Babiuc-Hamilton, Maria Cc: users@einsteintoolkit.org Subject: Re: Follow-up: [Users] How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS X Lion
Yes, I remember seeing that error too; although it may have only been with version 2.5 that I saw that.
So apparently some other libraries also used to be native, and are no longer, and I had already created the other links.
So in addition to lipmpi*, you'll also want to do
% cd /usr/lib/; sudo ln -s /opt/local/lib/libopen-pal* /opt/local/lib/libopen-rte* .
Let me know if that helps.
On 5/21/12 2:11 PM, "Babiuc-Hamilton, Maria" babiuc@marshall.edu wrote:
Scott,
I finally got around to check follow your instructions, but I ran into this problem:
Parsed document of type Plugin
Plugin: CarpetHDF5 ("Carpet AMR/curvilinear HDF5 output generated by the Cactus Computational Toolkit", type=database) -- version 2.1 Attribute: ()
-- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Checking whether CXX compiler has -isysroot -- Checking whether CXX compiler has -isysroot - yes -- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done CMake Error at CMakeLists.txt:90 (VISIT_PLUGIN_TARGET_RTOD): Unknown CMake command "VISIT_PLUGIN_TARGET_RTOD".
-- Configuring incomplete, errors occurred! make: *** No targets specified and no makefile found. Stop.
The only difference was that I did a ./configure --enable-cxx first in my hdf5-1.8.9 directory.
Could you please help me out?
Christian, do you have any suggestions?
thanks, Maria ________________________________________ From: Babiuc-Hamilton, Maria Sent: Tuesday, May 15, 2012 8:42 AM To: Scott Hawley Subject: Re: [Users] How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS X Lion
Scott,
Fantastic! I'll try it right away! I had problems making Visit work with MacOS last year, and had to do my own little hack, but haven't use it for a while, because I was afraid that if I upgrade I'll run into problems again. Have had any success with ygraph?
Cheers, Maria
On 5/14/12 5:23 PM, "Scott Hawley" scott.hawley@belmont.edu wrote:
Here's what I did:
- Downloaded the 64-bit binary of Visit 2.4.2 from the Visit web site
- Downloaded the CarpetHDF directory via svn.
- Downloaded hdf5-1.8.9 source via ftp. I just put it in the
CarpetHDF5 directory. Did a make and make installŠ. "HDF5 Directory" is then .../hdf5-1.8.9/hdf5/ (see below) 4. Made sure "Remote Login" is enabled under "Sharing" in "System Preferences". Visit uses this. Went ahead and did a "ssh localhost" just to make sure. I was actually prompted to confirm an address because I'm on LSU's network right now. (Presumably Visit needs a clean login with no pesky questions or password prompts.) 5. Created symbolic links in /usr/lib to whichever MPI libraries I planned to use. Older versions of OS X had native MPI support, and this is hard coded in the binary you get from the visit site. I use OpenMPI and MacPorts, so I went to /usr/lib and did "sudo ln -s /opt/local/lib/libmpi* ." 6. Deleted my ~/.visit directory entirely. This may not be necessary. 7. Went in the CarpetHDF5 and ran ./install and Šbasically just did what was in the readme, that is: in the xmledit window, clicked on "Cmake" and then updated the flags, as in
CXXFLAGS = -I/Applications/VisIt.app/Contents/Resources/2.4.2/darwin-x86_64/includ e -I/Users/shawley/apps/VizTools/CarpetHDF5/hdf5-1.8.9/hdf5/include LDFLAGS = -L/Applications/VisIt.app/Contents/Resources/2.4.2/darwin-x86_64/lib -L/Users/shawley/apps/VizTools/CarpetHDF5/hdf5-1.8.9/hdf5/lib Saved and closed the window, let it do its thing... 8. Ran visit from the command line, using the -noconfig option. The latest version of Visit has a problem with "localhost" on Mac, for some reason. so visit -noconfig
..and then visit came up, I opened a .h5 file and was able to do all the usual things with it!
Good luck! -Scott
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Hello,
i installed visit from source on my imac running mac osx lion (in order to get the parallel engine working) as well as the CarpetHDF5 plugin, and everything works...in case anyone is interested i could summarize the crucial steps i took in order to make it work for you..
best wishes,
Vassili
On Tue, May 22, 2012 at 9:57 PM, Scott Hawley scott.hawley@belmont.eduwrote:
Maria, No there are only a few libopen-rte files you can unlink if you want.
I noticed that these errors are coming from /usr/local/lib, which is not a location I've used. I put the links in /usr/lib.
On 5/22/12 9:06 AM, "Babiuc-Hamilton, Maria" babiuc@marshall.edu wrote:
Scott,
Yes, I did. The error I am getting now when configuring Cactus is: dyld: Symbol not found: _orte_ess Referenced from: /usr/local/lib/libmpi.0.dylib Expected in: /usr/local/lib/libopen-rte.0.dylib in /usr/local/lib/libmpi.0.dylib
Looking on the web, it seems that other Apple users had this problem when trying to link libraries. I'm afraid that I made this mess when I linked libopen-rte*? Is there a clean and quick fix, or I need to reinstall my whole operating system? :O
Please help! Maria
From: Scott Hawley [scott.hawley@belmont.edu] Sent: Monday, May 21, 2012 4:05 PM To: Babiuc-Hamilton, Maria Cc: users@einsteintoolkit.org Subject: Re: Follow-up: [Users] How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS X Lion
You compiled the CarpetHDF plugin like I said, and are running visit with -noconfig?
On 5/21/12 3:03 PM, "Babiuc-Hamilton, Maria" babiuc@marshall.edu wrote:
Thanks. I just downgraded to Visit 2.4.2 and now it looked like I got rid of that error. However, when trying to see a h5 file, I got the error:
The metadata server running on host localhost has exited abnormally. VisIt is trying to restart it.
Shortly thereafter, the following occured...
VisIt was unable to open "/Users/student/Cactus/VizTools/ks-mclachlan_metric.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the underlying file format has changed and VisIt's readers have not been updated yet, or when the reader VisIt is using for your file format is not robust. Please check whether the file is corrupted and, if not, contact a VisIt developer.
Moreover, when I am trying to run Cactus, I am getting this:
./cactus_tov tov.rpar dyld: Symbol not found: __ZN3MPI3Win14Set_errhandlerERKNS_10ErrhandlerE Referenced from: /Users/student/Cactus/exe/./cactus_tov Expected in: /usr/lib/libmpi_cxx.0.dylib
Trace/BPT trap
I checked, and I do have /usr/lib/libmpi_cxx.0.dylib Any ideas?
thanks, Maria
From: Scott Hawley [scott.hawley@belmont.edu] Sent: Monday, May 21, 2012 3:18 PM To: Babiuc-Hamilton, Maria Cc: users@einsteintoolkit.org Subject: Re: Follow-up: [Users] How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS X Lion
Yes, I remember seeing that error too; although it may have only been with version 2.5 that I saw that.
So apparently some other libraries also used to be native, and are no longer, and I had already created the other links.
So in addition to lipmpi*, you'll also want to do
% cd /usr/lib/; sudo ln -s /opt/local/lib/libopen-pal* /opt/local/lib/libopen-rte* .
Let me know if that helps.
On 5/21/12 2:11 PM, "Babiuc-Hamilton, Maria" babiuc@marshall.edu
wrote:
Scott,
I finally got around to check follow your instructions, but I ran into this problem:
Parsed document of type Plugin
Plugin: CarpetHDF5 ("Carpet AMR/curvilinear HDF5 output generated by the Cactus Computational Toolkit", type=database) -- version 2.1 Attribute: ()
-- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Checking whether CXX compiler has -isysroot -- Checking whether CXX compiler has -isysroot - yes -- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done CMake Error at CMakeLists.txt:90 (VISIT_PLUGIN_TARGET_RTOD): Unknown CMake command "VISIT_PLUGIN_TARGET_RTOD".
-- Configuring incomplete, errors occurred! make: *** No targets specified and no makefile found. Stop.
The only difference was that I did a ./configure --enable-cxx first in my hdf5-1.8.9 directory.
Could you please help me out?
Christian, do you have any suggestions?
thanks, Maria ________________________________________ From: Babiuc-Hamilton, Maria Sent: Tuesday, May 15, 2012 8:42 AM To: Scott Hawley Subject: Re: [Users] How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS X Lion
Scott,
Fantastic! I'll try it right away! I had problems making Visit work with MacOS last year, and had to do my own little hack, but haven't use it for a while, because I was afraid that if I upgrade I'll run into problems again. Have had any success with ygraph?
Cheers, Maria
On 5/14/12 5:23 PM, "Scott Hawley" scott.hawley@belmont.edu wrote:
Here's what I did:
- Downloaded the 64-bit binary of Visit 2.4.2 from the Visit web site
- Downloaded the CarpetHDF directory via svn.
- Downloaded hdf5-1.8.9 source via ftp. I just put it in the
CarpetHDF5 directory. Did a make and make installŠ. "HDF5 Directory" is then .../hdf5-1.8.9/hdf5/ (see below) 4. Made sure "Remote Login" is enabled under "Sharing" in "System Preferences". Visit uses this. Went ahead and did a "ssh localhost" just to make sure. I was actually prompted to confirm an address because I'm on LSU's network right now. (Presumably Visit needs a clean login with no pesky questions or password prompts.) 5. Created symbolic links in /usr/lib to whichever MPI libraries I planned to use. Older versions of OS X had native MPI support, and this is hard coded in the binary you get from the visit site. I use OpenMPI and MacPorts, so I went to /usr/lib and did "sudo ln -s /opt/local/lib/libmpi* ." 6. Deleted my ~/.visit directory entirely. This may not be necessary. 7. Went in the CarpetHDF5 and ran ./install and Šbasically just did what was in the readme, that is: in the xmledit window, clicked on "Cmake" and then updated the flags, as in
CXXFLAGS = -I/Applications/VisIt.app/Contents/Resources/2.4.2/darwin-x86_64/includ e -I/Users/shawley/apps/VizTools/CarpetHDF5/hdf5-1.8.9/hdf5/include LDFLAGS = -L/Applications/VisIt.app/Contents/Resources/2.4.2/darwin-x86_64/lib -L/Users/shawley/apps/VizTools/CarpetHDF5/hdf5-1.8.9/hdf5/lib Saved and closed the window, let it do its thing... 8. Ran visit from the command line, using the -noconfig option. The latest version of Visit has a problem with "localhost" on Mac, for some reason. so visit -noconfig
..and then visit came up, I opened a .h5 file and was able to do all the usual things with it!
Good luck! -Scott
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
users@lists.einsteintoolkit.org
-
Babiuc-Hamilton, Maria -
Scott Hawley -
Vassilios Mewes